clusterData-class {goCluster} | R Documentation

## Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.

### Description

This class provides a container for microarray data.

### Details

This class provides a wrapper for `exprSet` objects from bioconductor. It provides a link to the annotation data in goCluster. A vector of unique ids that connects each element (row) in the dataset with its corresponding annotation terms has to be provided.

### Slots

`name`:
  Object of class `"character"`, a name for the dataset.
`dataset`:
  Object of class `"exprSet"`, the dataset for the analysis.
`uniqueid`:
  Object of class `"character"`, the unique id for each gene (row) in the dataset.
`anno`:
  Object of class `"clusterAnnotation"`, the annotation object that holds the annotation to this dataset.

Additional slots are described in the documentation of the `clusterModule-class`.

### Extends

Class `"clusterModule"`, directly.

### Methods

config
  `signature(object = "clusterData")`: interactive setup of the class.
setup
  `signature(object = "clusterData")`: returns the configuration (including the dataset) of the object as a list. This list can be used for the non-interactive setup of the class.
setup<-
  `signature(object = "clusterData")`: non-interactive setup of the class. The options are specified using a list.
execute
  `signature(object = "clusterData")`: passes the `execute`-call to the annotation object.
execute<-
  `signature(object = "clusterData")`: passes the `execute<-`-call to the annotation object.
reset
  `signature(object = "clusterData")`: This only conveys the reset signal to the clusterAnnotation object. The dataset of the clusterData object will not be removed by this reset method. A new `goCluster`-object should be created for each new dataset.
print
  `signature(object = "clusterData")`: calls the print function of the exprSet-object stored in the dataset slot.

### Author(s)

Gunnar Wrobel, http://www.gunnarwrobel.de.

### See Also

`goCluster-class`, `clusterAnnotation-class`, `setup`, `setup<-`, `execute`, `reset`.

[Package goCluster version 1.0.3 Index]